[phenixbb] N-linked glycans in phenix.refine

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Sep 30 08:35:47 PDT 2009

> > Thanks so much for the update.  You were right.
> > Now I have another problem, maybe you know.  I am
> > using a NAG without the O1 and the program is trying to delete and stop
> >
> > RuntimeError: delete_atom_in_place: unknown atom_id: O1

It is trying to delete the O1 from the cif definitions, probably
because of ...

> >       data_link: NAG-ASN
> >         mod_id_1: DEL-O1
> >         mod_id_2: DEL-HD22

... the associated "DEL-O1" modification. If your NAG cif file doesn't
have the O1 it is probably easiest to copy and rename the link.
You can find the link in the file shown via



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